Background Ductal carcinoma in situ (DCIS) display favorable outcome but little is known about the factors associated with invasive recurrence. To identify better prognostic biomarkers, we performed gene expression analysis followed by immunohistochemistry (IHC) staining validation. Methods Differential gene expression (DGE) analysis of 24 pure DCIS patients was performed using a nanostring platform. RNA was extracted from paraffin blocks from age/estrogen receptor matched recurrence-free (n=16) and invasive-recurrence (n=8) cases (disease-free interval >5 years). External validation was done among independent 61 cases, invasive-recurrence (n=16) and recurrence-free (n=45) pure DCIS cases by IHC staining. Results Eight differentially expressed genes were found statistically significant (log 2-fold change <–1 or >1 and p<0.001). Less than ½ fold expression of CUL1, AR, RPS27A, CTNNB1, MAP3K1, PRKACA, GNG12, MGMT genes were observed in REC cases compared to NED cases. Androgen receptor (AR) and histone deacetylase 1 (HDAC1) were selected for external validation (AR: log 2-fold change –1.35, p<0.001, and HDAC1; log 2-fold change –0.774, p<0.001). AR and HDAC1 protein expression was externally validated by IHC staining of 61 pure DCIS cases (16 invasive-recurrence versus 45 recurrence-free). Absence of AR and high HDAC1 expression was an independent risk factor for invasive recurrence (hazard ratio 5.04, 95% CI: 1.24, 20.4; p=0.023, hazard ratio 3.07, 95% CI: 1.04, 9.04; p=0.042). High nuclear grade (NG 3) was also associated with long term invasive recurrence. Conclusion Comparative gene expression analysis of pure DCIS revealed 8 genes differentially expressed among recurred cases. Immunohistochemistry validation within an independent cohort suggests that, absence of AR and overexpression of HDAC1 was associated with greater risk of long term invasive recurrence among pure DCIS.